The quantitative contribution of tropical estuaries to the atmospheric CO2 budget has large uncertainties, both spatially and seasonally. We investigated the seasonal and spatial variations of carbon biogeochemistry downstream of Ho Chi Minh City (Southern Vietnam). We sampled four sites distributed from downstream of a highly urbanised watershed through mangroves to the South China Sea coast during the dry and wet seasons. Measured partial pressure of CO2(pCO2) ranged from 660 to 3000 μatm during the dry season, and from 740 to 5000 μatm during the wet season. High organic load, dissolved oxygen saturation down to 17%, and pCO2up to 5000 μatm at the freshwater endmember of the estuary reflected the intense human pressure on this ecosystem. We show that releases from mangrove soils affect the water column pCO2 in this large tropical estuary (~600 m wide and 10–20 m deep). This study is among the few to report direct measurements of both water pCO2 and CO2 emissions in a Southeast Asian tropical estuary located in a highly urbanised watershed. It shows that the contribution of such estuaries may have been previously underestimated, with CO2 emissions ranging from 74 to 876 mmol m−2 day−1 at low current velocity (< 0.2 m s−1). Corresponding gas transfer velocities k600, ranging from 1.7 to 11.0 m day−1, were about 2 to 4 times of k600 estimated using published literature equations.